Smith Waterman in C

higgins at higgins at
Tue Jul 9 07:01:23 EST 1996

In article <31E18A8A.41C6 at>, Hemant Varma <varma at> writes:
> Hello Folks,
> 	     I am looking for a C implementation of 
> Smith -Waterman algorithm for sequence alignment. If
> anybody could please indicate where I can find such a
> program, I would really appreciate it. 
>  Thank you,
> Hemant
> -- 

Hi Hemant:

SSEARCH in Bill Pearson's FASTA package is a C program for a S+W search.
This code is for searching/aligning a query sequence against an entire database
using the S+W algorithm. 

Get it by ftp:

      "A revised version of FASTA3.0 - fasta30t4.shar.Z is available from in pub/fasta."

Des Higgins 
EMBL/EBI, Hinxton, UK.

> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> Hemant Varma                                                                          
> Lawrence Livermore National Lab. 		 
> Livermore CA 94550
> (510)423 5065

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